match.lib.plinkscorefiles
=========================

.. py:module:: match.lib.plinkscorefiles

.. autoapi-nested-parse::

   This module contains the PlinkScoreFiles class, which represents one or more
   scoring files ready to be used with plink2 --score



Attributes
----------

.. autoapisummary::

   match.lib.plinkscorefiles.logger


Classes
-------

.. autoapisummary::

   match.lib.plinkscorefiles.PlinkScoreFiles


Module Contents
---------------

.. py:class:: PlinkScoreFiles(*elements)



   Represents a sequence of scoring files written by :class:`MatchResults`


   .. py:method:: merge(directory)

      Merge scoring files without recomputing matches

      Assumes a standard file naming system was used: ``dataset_chrom_effecttype_n``

      >>> import tempfile, os, glob
      >>> from ._config import Config
      >>> from .variantframe import VariantFrame
      >>> from .scoringfileframe import ScoringFileFrame, match_variants
      >>> from .matchresult import MatchResult, MatchResults
      >>> fout = tempfile.NamedTemporaryFile(delete=False)
      >>> target_path = Config.ROOT_DIR / "tests" / "data" / "good_match.pvar"
      >>> score_path =  Config.ROOT_DIR / "tests" / "data" / "good_match_scorefile.txt"
      >>> target = VariantFrame(target_path, dataset="goodmatch")
      >>> scorefile = ScoringFileFrame(score_path)
      >>> with target as target_df, scorefile as score_df:
      ...     results = match_variants(score_df=score_df, target_df=target_df, target=target)
      ...     _ = results.collect(outfile=fout.name)
      >>> x = MatchResult.from_ipc(fout.name, dataset="goodmatch")
      >>> foutdir = tempfile.mkdtemp()
      >>> with scorefile as score_df:
      ...     _ = MatchResults(x).write_scorefiles(directory=foutdir, split=True, score_df=score_df)  # doctest: +ELLIPSIS
      >>> plink_files = (pathlib.Path(foutdir) / x for x in os.listdir(foutdir))
      >>> psf = PlinkScoreFiles(*plink_files)
      >>> psf  # doctest: +ELLIPSIS
      PlinkScoreFiles([PosixPath('.../goodmatch_1_additive_0.scorefile.gz'), ...])
      >>> psf.merge(foutdir)
      >>> combined_paths = sorted(glob.glob(foutdir + "/*ALL*"),  key=lambda x: pathlib.Path(x).stem)
      >>> len(combined_paths)
      3
      >>> combined_paths # doctest: +ELLIPSIS
      ['.../goodmatch_ALL_additive_0.scorefile.gz', '.../goodmatch_ALL_dominant_0.scorefile.gz', '.../goodmatch_ALL_recessive_0.scorefile.gz']




.. py:data:: logger